According to the common view, conscientious objection is grounded in autonomy and is tolerated out of respect for the objector's autonomy. Emphasising autonomy as a central concept within the issue of conscientious objection implies that the conscientious objector has an independent choice among alternative beliefs, positions or values. In this paper, it is argued that: (a) it is not true that the typical conscientious objector has such a choice when they decide to act upon their conscience and (b) it is not true that the typical conscientious objector exercises autonomy when developing or acquiring their conscience. Therefore, tolerating conscientious objection does not reflect respect for the conscientious objector's right to choose but rather acknowledges their lack of real ability to choose their conscience and to refrain from acting upon their conscience. This has both normative and analytical implications for the treatment of conscientious objectors.